create_sequences {universalmotif}R Documentation

Create random sequences.

Description

Generate random sequences from any set of characters, represented as XStringSet objects.

Usage

create_sequences(alphabet = "DNA", seqnum = 100, seqlen = 100, freqs,
  progress = FALSE, BP = FALSE, nthreads = 1,
  rng.seed = sample.int(1e+09, 1))

Arguments

alphabet

character(1) One of c('DNA', 'RNA', 'AA'), or a string of characters to be used as the alphabet.

seqnum

numeric(1) Number of sequences to generate.

seqlen

numeric(1) Length of random sequences.

freqs

numeric A named vector of probabilities. The length of the vector must be the power of the number of letters in the sequence alphabet.

progress

logical(1) Deprecated. Does nothing.

BP

logical(1) Deprecated. See nthreads.

nthreads

numeric(1) Run create_sequences() in parallel with nthreads threads. nthreads = 0 uses all available threads. Note that no speed up will occur for jobs with seqnum = 1.

rng.seed

numeric(1) Set random number generator seed. Since sequence creation can occur simultaneously in multiple threads using C++, it cannot communicate with the regular R random number generator state and thus requires an independent seed. Each individual sequence creation instance is given the following seed: rng.seed * index. The default is to pick a random number as chosen by sample(), which effectively is make create_sequences() dependent on the R RNG state.

Value

XStringSet The returned sequences are unnamed.

Author(s)

Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca

See Also

create_motif(), shuffle_sequences()

Examples

## create DNA sequences with slightly increased AT content:
sequences <- create_sequences(freqs = c(A=0.3, C=0.2, G=0.2, T=0.3))
## create custom sequences:
sequences.QWER <- create_sequences("QWER")
## you can include non-alphabet characters are well, even spaces:
sequences.custom <- create_sequences("!@#$ ")


[Package universalmotif version 1.4.10 Index]